How to compare ESTs with assembled contigs of the genome?

[Godevil]

Hello,

I'm performing the genome assemlby, and I've already assembled reads into contigs. I want to compare ESTs with those contigs in order to estimate the accuracy of the assembly.

Could anyone recommend some software to me? At least I want to find how many percentage of those ESTs can math to the contigs.

Thank you very much!

[Wallysb01]

Hello,

I'm performing the genome assemlby, and I've already assembled reads into contigs. I want to compare ESTs with those contigs in order to estimate the accuracy of the assembly.

Could anyone recommend some software to me? At least I want to find how many percentage of those ESTs can math to the contigs.

Thank you very much!

Why not just use blast and have a pretty high cut off to assume they matched well?

[renesh]

You should use standlone NCBI Blast tool for finding the coverage of assembly.

[JackieBadger]

BLAT aligns RNA to DNA, taking into consideration splicing sites and is significantly faster than BLAST (http://genome.ucsc.edu/FAQ/FAQblat.html).

I am currently looking to employ BFAST (http://sourceforge.net/apps/mediawik...itle=Main_Page). Seems to have a much better literature associated with it, and is even faster than BLAT